This is a test version of Biostars. For the public version, visit https://www.biostars.org.
What is the maximum size of fasta file i can use for repeatmasker?

Hi all,

I'm having hard time to quantify repetitive elements through repeat masker. My each files are max 15 gb fasta. Whenever i run, my jobs were getting killed by PBS. I'm using 32 GB RAM. Do you think it is enough or do i have to increase the RAM. can you guys suggest something?

rnaseq repeatmasker repititive elements
• 1,813 views • link
written by PK • PK

You should include the parameters you're using and the error message.

• 0 views • link
written by Buffo Buffo 
RepeatMasker -s -nolow -species human -dir /out/put/repeat_counts -a -inv -pa 32 -lcambig -small -source -html -gff /inpuy/test.fasta

When i execute above mentioned command i'm getting the following error message

/var/spool/pbs/jobs/job_id: line 14: 2966220 Killed RepeatMasker -s -nolow -species human -dir /out/put/repeat_counts -a -inv -pa 32 -lcambig -small -source -html -gff /inpuy/test.fasta

If you need more information please ask me

• 0 views • link
written by PK • PK

RepetaMasker doesn't use too much mem, are you setting the MaxMem in your PBS command?

• 0 views • link
written by JC JC

I never used that option. This is the command i use to submit my job

qsub -l select=1:ncpus=32:ompthreads=32:mem=40gb:scratch_local=150gb -l walltime=24:00:00 ./my_script.sh
• 0 views • link
written by PK • PK

0 answers

No answers yet.

Log in to answer this question.

More posts like this